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Bioinformatics Advance Access published online on August 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl461
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© 2006 The Author(s)
Received July 18, 2006
Revised August 22, 2006
Accepted August 23, 2006

Applications note

Bio3d: an R package for the comparative analysis of protein structures

Barry J. Grant 1 *, Ana P. C. Rodrigues 2, Karim M. ElSawy 3, J. Andrew McCammon 4, and Leo S. D. Caves 3

1 Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
2 The Burnham Institute for Medical Research, La Jolla, CA 92037, USA
3 Department of Biology, University of York, York YO10 5YW, UK
4 Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute

* To whom correspondence should be addressed.
Barry J. Grant, E-mail: bgrant{at}mccammon.ucsd.edu


  Abstract

Summary: An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for the analysis of protein structural evolution. The method is implemented in bio3d, an R package for the exploratory analysis of structure and sequence data.

Availability: The bio3d package is distributed with full source code as a platform independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/.

Associate Editor: Anna Tramontano
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